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Merge pull request #40 from OHDSI/v5.1 

V5.1
This commit is contained in:
clairblacketer 2017-06-13 15:10:25 -04:00 committed by GitHub
parent e56f42ede1 7525f2a171
commit 31e72c2d0c
4 changed files with 431 additions and 356 deletions
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38
Oracle/OMOP CDM ddl - Oracle.sql
View File

@ -229,7 +229,7 @@ CREATE TABLE person
year_of_birth INTEGER NOT NULL , year_of_birth INTEGER NOT NULL ,
month_of_birth INTEGER NULL, month_of_birth INTEGER NULL,
day_of_birth INTEGER NULL, day_of_birth INTEGER NULL,
time_of_birth VARCHAR(10) NULL, birth_datetime TIMESTAMP WITH TIME ZONE NULL,
race_concept_id INTEGER NOT NULL, race_concept_id INTEGER NOT NULL,
ethnicity_concept_id INTEGER NOT NULL, ethnicity_concept_id INTEGER NOT NULL,
location_id INTEGER NULL, location_id INTEGER NULL,
@ -254,7 +254,9 @@ CREATE TABLE observation_period
observation_period_id INTEGER NOT NULL , observation_period_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
observation_period_start_date DATE NOT NULL , observation_period_start_date DATE NOT NULL ,
observation_period_start_datetime TIMESTAMP WITH TIME ZONE NOT NULL ,
observation_period_end_date DATE NOT NULL , observation_period_end_date DATE NOT NULL ,
observation_period_end_datetime TIMESTAMP WITH TIME ZONE NOT NULL ,
period_type_concept_id INTEGER NOT NULL period_type_concept_id INTEGER NOT NULL
) )
; ;
@ -268,7 +270,7 @@ CREATE TABLE specimen
specimen_concept_id INTEGER NOT NULL , specimen_concept_id INTEGER NOT NULL ,
specimen_type_concept_id INTEGER NOT NULL , specimen_type_concept_id INTEGER NOT NULL ,
specimen_date DATE NOT NULL , specimen_date DATE NOT NULL ,
specimen_time VARCHAR(10) NULL , specimen_datetime TIMESTAMP WITH TIME ZONE NULL ,
quantity FLOAT NULL , quantity FLOAT NULL ,
unit_concept_id INTEGER NULL , unit_concept_id INTEGER NULL ,
anatomic_site_concept_id INTEGER NULL , anatomic_site_concept_id INTEGER NULL ,
@ -287,7 +289,8 @@ CREATE TABLE death
( (
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
death_date DATE NOT NULL , death_date DATE NOT NULL ,
death_type_concept_id INTEGER NOT NULL , death_datetime TIMESTAMP WITH TIME ZONE NULL ,
death_type_concept_id INTEGER NOT NULL ,
cause_concept_id INTEGER NULL , cause_concept_id INTEGER NULL ,
cause_source_value VARCHAR(50) NULL, cause_source_value VARCHAR(50) NULL,
cause_source_concept_id INTEGER NULL cause_source_concept_id INTEGER NULL
@ -302,9 +305,9 @@ CREATE TABLE visit_occurrence
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
visit_concept_id INTEGER NOT NULL , visit_concept_id INTEGER NOT NULL ,
visit_start_date DATE NOT NULL , visit_start_date DATE NOT NULL ,
visit_start_time VARCHAR(10) NULL , visit_start_datetime TIMESTAMP WITH TIME ZONE NULL ,
visit_end_date DATE NOT NULL , visit_end_date DATE NOT NULL ,
visit_end_time VARCHAR(10) NULL , visit_end_datetime TIMESTAMP WITH TIME ZONE NULL ,
visit_type_concept_id INTEGER NOT NULL , visit_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL, provider_id INTEGER NULL,
care_site_id INTEGER NULL, care_site_id INTEGER NULL,
@ -321,6 +324,7 @@ CREATE TABLE procedure_occurrence
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
procedure_concept_id INTEGER NOT NULL , procedure_concept_id INTEGER NOT NULL ,
procedure_date DATE NOT NULL , procedure_date DATE NOT NULL ,
procedure_datetime TIMESTAMP WITH TIME ZONE NOT NULL ,
procedure_type_concept_id INTEGER NOT NULL , procedure_type_concept_id INTEGER NOT NULL ,
modifier_concept_id INTEGER NULL , modifier_concept_id INTEGER NULL ,
quantity INTEGER NULL , quantity INTEGER NULL ,
@ -340,8 +344,10 @@ CREATE TABLE drug_exposure
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL , drug_concept_id INTEGER NOT NULL ,
drug_exposure_start_date DATE NOT NULL , drug_exposure_start_date DATE NOT NULL ,
drug_exposure_end_date DATE NULL , drug_exposure_start_datetime TIMESTAMP WITH TIME ZONE NOT NULL ,
drug_type_concept_id INTEGER NOT NULL , drug_exposure_end_date DATE NULL ,
drug_exposure_end_datetime TIMESTAMP WITH TIME ZONE NULL ,
drug_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL , stop_reason VARCHAR(20) NULL ,
refills INTEGER NULL , refills INTEGER NULL ,
quantity FLOAT NULL , quantity FLOAT NULL ,
@ -367,8 +373,10 @@ CREATE TABLE device_exposure
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
device_concept_id INTEGER NOT NULL , device_concept_id INTEGER NOT NULL ,
device_exposure_start_date DATE NOT NULL , device_exposure_start_date DATE NOT NULL ,
device_exposure_end_date DATE NULL , device_exposure_start_datetime TIMESTAMP WITH TIME ZONE NOT NULL ,
device_type_concept_id INTEGER NOT NULL , device_exposure_end_date DATE NULL ,
device_exposure_end_datetime TIMESTAMP WITH TIME ZONE NULL ,
device_type_concept_id INTEGER NOT NULL ,
unique_device_id VARCHAR(50) NULL , unique_device_id VARCHAR(50) NULL ,
quantity INTEGER NULL , quantity INTEGER NULL ,
provider_id INTEGER NULL , provider_id INTEGER NULL ,
@ -385,8 +393,10 @@ CREATE TABLE condition_occurrence
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
condition_concept_id INTEGER NOT NULL , condition_concept_id INTEGER NOT NULL ,
condition_start_date DATE NOT NULL , condition_start_date DATE NOT NULL ,
condition_end_date DATE NULL , condition_start_datetime TIMESTAMP WITH TIME ZONE NOT NULL ,
condition_type_concept_id INTEGER NOT NULL , condition_end_date DATE NULL ,
condition_end_datetime TIMESTAMP WITH TIME ZONE NULL ,
condition_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL , stop_reason VARCHAR(20) NULL ,
provider_id INTEGER NULL , provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id INTEGER NULL ,
@ -403,7 +413,7 @@ CREATE TABLE measurement
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
measurement_concept_id INTEGER NOT NULL , measurement_concept_id INTEGER NOT NULL ,
measurement_date DATE NOT NULL , measurement_date DATE NOT NULL ,
measurement_time VARCHAR(10) NULL , measurement_datetime TIMESTAMP WITH TIME ZONE NULL ,
measurement_type_concept_id INTEGER NOT NULL , measurement_type_concept_id INTEGER NOT NULL ,
operator_concept_id INTEGER NULL , operator_concept_id INTEGER NULL ,
value_as_number FLOAT NULL , value_as_number FLOAT NULL ,
@ -427,7 +437,7 @@ CREATE TABLE note
note_id INTEGER NOT NULL , note_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
note_date DATE NOT NULL , note_date DATE NOT NULL ,
note_time VARCHAR(10) NULL , note_datetime TIMESTAMP WITH TIME ZONE NULL ,
note_type_concept_id INTEGER NOT NULL , note_type_concept_id INTEGER NOT NULL ,
note_text CLOB NOT NULL , note_text CLOB NOT NULL ,
provider_id INTEGER NULL , provider_id INTEGER NULL ,
@ -444,7 +454,7 @@ CREATE TABLE observation
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
observation_concept_id INTEGER NOT NULL , observation_concept_id INTEGER NOT NULL ,
observation_date DATE NOT NULL , observation_date DATE NOT NULL ,
observation_time VARCHAR(10) NULL , observation_datetime TIMESTAMP WITH TIME ZONE NULL ,
observation_type_concept_id INTEGER NOT NULL , observation_type_concept_id INTEGER NOT NULL ,
value_as_number FLOAT NULL , value_as_number FLOAT NULL ,
value_as_string VARCHAR(60) NULL , value_as_string VARCHAR(60) NULL ,

38
PostgreSQL/OMOP CDM ddl - PostgreSQL.sql
View File

@ -229,7 +229,7 @@ CREATE TABLE person
year_of_birth INTEGER NOT NULL , year_of_birth INTEGER NOT NULL ,
month_of_birth INTEGER NULL, month_of_birth INTEGER NULL,
day_of_birth INTEGER NULL, day_of_birth INTEGER NULL,
time_of_birth VARCHAR(10) NULL, birth_datetime TIMESTAMP NULL,
race_concept_id INTEGER NOT NULL, race_concept_id INTEGER NOT NULL,
ethnicity_concept_id INTEGER NOT NULL, ethnicity_concept_id INTEGER NOT NULL,
location_id INTEGER NULL, location_id INTEGER NULL,
@ -254,7 +254,9 @@ CREATE TABLE observation_period
observation_period_id INTEGER NOT NULL , observation_period_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
observation_period_start_date DATE NOT NULL , observation_period_start_date DATE NOT NULL ,
observation_period_start_datetime TIMESTAMP NOT NULL ,
observation_period_end_date DATE NOT NULL , observation_period_end_date DATE NOT NULL ,
observation_period_end_datetime TIMESTAMP NOT NULL ,
period_type_concept_id INTEGER NOT NULL period_type_concept_id INTEGER NOT NULL
) )
; ;
@ -268,7 +270,7 @@ CREATE TABLE specimen
specimen_concept_id INTEGER NOT NULL , specimen_concept_id INTEGER NOT NULL ,
specimen_type_concept_id INTEGER NOT NULL , specimen_type_concept_id INTEGER NOT NULL ,
specimen_date DATE NOT NULL , specimen_date DATE NOT NULL ,
specimen_time VARCHAR(10) NULL , specimen_datetime TIMESTAMP NULL ,
quantity NUMERIC NULL , quantity NUMERIC NULL ,
unit_concept_id INTEGER NULL , unit_concept_id INTEGER NULL ,
anatomic_site_concept_id INTEGER NULL , anatomic_site_concept_id INTEGER NULL ,
@ -287,7 +289,8 @@ CREATE TABLE death
( (
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
death_date DATE NOT NULL , death_date DATE NOT NULL ,
death_type_concept_id INTEGER NOT NULL , death_datetime TIMESTAMP NULL ,
death_type_concept_id INTEGER NOT NULL ,
cause_concept_id INTEGER NULL , cause_concept_id INTEGER NULL ,
cause_source_value VARCHAR(50) NULL, cause_source_value VARCHAR(50) NULL,
cause_source_concept_id INTEGER NULL cause_source_concept_id INTEGER NULL
@ -302,9 +305,9 @@ CREATE TABLE visit_occurrence
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
visit_concept_id INTEGER NOT NULL , visit_concept_id INTEGER NOT NULL ,
visit_start_date DATE NOT NULL , visit_start_date DATE NOT NULL ,
visit_start_time VARCHAR(10) NULL , visit_start_datetime TIMESTAMP NULL ,
visit_end_date DATE NOT NULL , visit_end_date DATE NOT NULL ,
visit_end_time VARCHAR(10) NULL , visit_end_datetime TIMESTAMP NULL ,
visit_type_concept_id INTEGER NOT NULL , visit_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL, provider_id INTEGER NULL,
care_site_id INTEGER NULL, care_site_id INTEGER NULL,
@ -321,6 +324,7 @@ CREATE TABLE procedure_occurrence
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
procedure_concept_id INTEGER NOT NULL , procedure_concept_id INTEGER NOT NULL ,
procedure_date DATE NOT NULL , procedure_date DATE NOT NULL ,
procedure_datetime TIMESTAMP NOT NULL ,
procedure_type_concept_id INTEGER NOT NULL , procedure_type_concept_id INTEGER NOT NULL ,
modifier_concept_id INTEGER NULL , modifier_concept_id INTEGER NULL ,
quantity INTEGER NULL , quantity INTEGER NULL ,
@ -340,8 +344,10 @@ CREATE TABLE drug_exposure
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL , drug_concept_id INTEGER NOT NULL ,
drug_exposure_start_date DATE NOT NULL , drug_exposure_start_date DATE NOT NULL ,
drug_exposure_end_date DATE NULL , drug_exposure_start_datetime TIMESTAMP NOT NULL ,
drug_type_concept_id INTEGER NOT NULL , drug_exposure_end_date DATE NULL ,
drug_exposure_end_datetime TIMESTAMP NULL ,
drug_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL , stop_reason VARCHAR(20) NULL ,
refills INTEGER NULL , refills INTEGER NULL ,
quantity NUMERIC NULL , quantity NUMERIC NULL ,
@ -367,8 +373,10 @@ CREATE TABLE device_exposure
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
device_concept_id INTEGER NOT NULL , device_concept_id INTEGER NOT NULL ,
device_exposure_start_date DATE NOT NULL , device_exposure_start_date DATE NOT NULL ,
device_exposure_end_date DATE NULL , device_exposure_start_datetime TIMESTAMP NOT NULL ,
device_type_concept_id INTEGER NOT NULL , device_exposure_end_date DATE NULL ,
device_exposure_end_datetime TIMESTAMP NULL ,
device_type_concept_id INTEGER NOT NULL ,
unique_device_id VARCHAR(50) NULL , unique_device_id VARCHAR(50) NULL ,
quantity INTEGER NULL , quantity INTEGER NULL ,
provider_id INTEGER NULL , provider_id INTEGER NULL ,
@ -385,8 +393,10 @@ CREATE TABLE condition_occurrence
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
condition_concept_id INTEGER NOT NULL , condition_concept_id INTEGER NOT NULL ,
condition_start_date DATE NOT NULL , condition_start_date DATE NOT NULL ,
condition_end_date DATE NULL , condition_start_datetime TIMESTAMP NOT NULL ,
condition_type_concept_id INTEGER NOT NULL , condition_end_date DATE NULL ,
condition_end_datetime TIMESTAMP NULL ,
condition_type_concept_id INTEGER NOT NULL ,
stop_reason VARCHAR(20) NULL , stop_reason VARCHAR(20) NULL ,
provider_id INTEGER NULL , provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id INTEGER NULL ,
@ -403,7 +413,7 @@ CREATE TABLE measurement
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
measurement_concept_id INTEGER NOT NULL , measurement_concept_id INTEGER NOT NULL ,
measurement_date DATE NOT NULL , measurement_date DATE NOT NULL ,
measurement_time VARCHAR(10) NULL , measurement_datetime TIMESTAMP NULL ,
measurement_type_concept_id INTEGER NOT NULL , measurement_type_concept_id INTEGER NOT NULL ,
operator_concept_id INTEGER NULL , operator_concept_id INTEGER NULL ,
value_as_number NUMERIC NULL , value_as_number NUMERIC NULL ,
@ -427,7 +437,7 @@ CREATE TABLE note
note_id INTEGER NOT NULL , note_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
note_date DATE NOT NULL , note_date DATE NOT NULL ,
note_time VARCHAR(10) NULL , note_datetime TIMESTAMP NULL ,
note_type_concept_id INTEGER NOT NULL , note_type_concept_id INTEGER NOT NULL ,
note_text TEXT NOT NULL , note_text TEXT NOT NULL ,
provider_id INTEGER NULL , provider_id INTEGER NULL ,
@ -444,7 +454,7 @@ CREATE TABLE observation
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
observation_concept_id INTEGER NOT NULL , observation_concept_id INTEGER NOT NULL ,
observation_date DATE NOT NULL , observation_date DATE NOT NULL ,
observation_time VARCHAR(10) NULL , observation_datetime TIMESTAMP NULL ,
observation_type_concept_id INTEGER NOT NULL , observation_type_concept_id INTEGER NOT NULL ,
value_as_number NUMERIC NULL , value_as_number NUMERIC NULL ,
value_as_string VARCHAR(60) NULL , value_as_string VARCHAR(60) NULL ,

45
README.md
View File

@ -1,6 +1,51 @@
Common-Data-Model Common-Data-Model
================= =================
v5.1
See full CDM specification file on our [Wiki](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:single-page) or in the [CDM V5 PDF](https://github.com/OHDSI/CommonDataModel/blob/master/OMOP%20CDM%20v5.pdf)
Release Notes
=============
This version is bases on this CDM working group [proposal](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:next_cdm:time). The proposed and accepted changes include adding a datetime field to every table that had a date column. These were the new columns added:
**PERSON**
* birth_datetime, not required
**SPECIMEN**
* specimen_datetime, not required
**DEATH**
* death_datetime, not required
**VISIT_OCCURRENCE**
* visit_start_datetime, not required
* visit_end_datetime, not required
**PROCEDURE_OCCURRENCE**
* procedure_datetime, not required
**DRUG_EXPOSURE**
* drug_exposure_start_datetime, not required
* drug_exposure_end_datetime, not required
**DEVICE_EXPOSURE**
* device_exposure_start_datetime, not required
* device_exposure_end_datetime, not required
**CONDITION_OCCURRENCE**
* condition_start_datetime, not required
* condition_end_datetime, not required
**MEASUREMENT**
* measurement_datetime as time, not required
**OBSERVATION**
* observation_datetime, not required
**NOTE**
* note_datetime, not required
=======
This repo contains the definition of the OMOP Common Data Model. It supports the 4 SQL technologies: Impala, Oracle, Postgres and SQL Server. For each, the DDL, constraints and indexes (if appropirate) are defined. This repo contains the definition of the OMOP Common Data Model. It supports the 4 SQL technologies: Impala, Oracle, Postgres and SQL Server. For each, the DDL, constraints and indexes (if appropirate) are defined.
Versions are defined using tagging and versioning. Full versions (V6, 7 etc.) are released irregularly after a major strategy change or use case coverage. It will be issued during an OHDSI Symposium. Major version (V5.1, 5.2 etc.) are released half yearly (1-Jul and 1-Jan). Those versions are not guaranteed to be backward compatible. Minor versions (V5.1.1, V5.1.2 etc.) are released irregularly and often, and contain small hot fixes or backward compatible changes to the last Major Version. Versions are defined using tagging and versioning. Full versions (V6, 7 etc.) are released irregularly after a major strategy change or use case coverage. It will be issued during an OHDSI Symposium. Major version (V5.1, 5.2 etc.) are released half yearly (1-Jul and 1-Jan). Those versions are not guaranteed to be backward compatible. Minor versions (V5.1.1, V5.1.2 etc.) are released irregularly and often, and contain small hot fixes or backward compatible changes to the last Major Version.

666
Sql Server/OMOP CDM ddl - SQL Server.sql
View File

@ -194,19 +194,19 @@ Standardized meta-data
***************************/ ***************************/
CREATE TABLE cdm_source CREATE TABLE cdm_source
( (
cdm_source_name VARCHAR(255) NOT NULL, cdm_source_name VARCHAR(255) NOT NULL,
cdm_source_abbreviation VARCHAR(25) NULL, cdm_source_abbreviation VARCHAR(25) NULL,
cdm_holder VARCHAR(255) NULL, cdm_holder VARCHAR(255) NULL,
source_description VARCHAR(MAX) NULL, source_description VARCHAR(MAX) NULL,
source_documentation_reference VARCHAR(255) NULL, source_documentation_reference VARCHAR(255) NULL,
cdm_etl_reference VARCHAR(255) NULL, cdm_etl_reference VARCHAR(255) NULL,
source_release_date DATE NULL, source_release_date DATE NULL,
cdm_release_date DATE NULL, cdm_release_date DATE NULL,
cdm_version VARCHAR(10) NULL, cdm_version VARCHAR(10) NULL,
vocabulary_version VARCHAR(20) NULL vocabulary_version VARCHAR(20) NULL
) )
; ;
@ -222,254 +222,264 @@ Standardized clinical data
************************/ ************************/
CREATE TABLE person CREATE TABLE person
( (
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
gender_concept_id INTEGER NOT NULL , gender_concept_id INTEGER NOT NULL ,
year_of_birth INTEGER NOT NULL , year_of_birth INTEGER NOT NULL ,
month_of_birth INTEGER NULL, month_of_birth INTEGER NULL,
day_of_birth INTEGER NULL, day_of_birth INTEGER NULL,
time_of_birth VARCHAR(10) NULL, birth_datetime DATETIME2 NULL,
race_concept_id INTEGER NOT NULL, race_concept_id INTEGER NOT NULL,
ethnicity_concept_id INTEGER NOT NULL, ethnicity_concept_id INTEGER NOT NULL,
location_id INTEGER NULL, location_id INTEGER NULL,
provider_id INTEGER NULL, provider_id INTEGER NULL,
care_site_id INTEGER NULL, care_site_id INTEGER NULL,
person_source_value VARCHAR(50) NULL, person_source_value VARCHAR(50) NULL,
gender_source_value VARCHAR(50) NULL, gender_source_value VARCHAR(50) NULL,
gender_source_concept_id INTEGER NULL, gender_source_concept_id INTEGER NULL,
race_source_value VARCHAR(50) NULL, race_source_value VARCHAR(50) NULL,
race_source_concept_id INTEGER NULL, race_source_concept_id INTEGER NULL,
ethnicity_source_value VARCHAR(50) NULL, ethnicity_source_value VARCHAR(50) NULL,
ethnicity_source_concept_id INTEGER NULL ethnicity_source_concept_id INTEGER NULL
) )
; ;
CREATE TABLE observation_period CREATE TABLE observation_period
( (
observation_period_id INTEGER NOT NULL , observation_period_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
observation_period_start_date DATE NOT NULL , observation_period_start_date DATE NOT NULL ,
observation_period_end_date DATE NOT NULL , observation_period_start_datetime DATETIME2 NOT NULL ,
period_type_concept_id INTEGER NOT NULL observation_period_end_date DATE NOT NULL ,
) observation_period_end_datetime DATETIME2 NOT NULL ,
period_type_concept_id INTEGER NOT NULL
)
; ;
CREATE TABLE specimen CREATE TABLE specimen
( (
specimen_id INTEGER NOT NULL , specimen_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
specimen_concept_id INTEGER NOT NULL , specimen_concept_id INTEGER NOT NULL ,
specimen_type_concept_id INTEGER NOT NULL , specimen_type_concept_id INTEGER NOT NULL ,
specimen_date DATE NOT NULL , specimen_date DATE NOT NULL ,
specimen_time VARCHAR(10) NULL , specimen_datetime DATETIME2 NULL ,
quantity FLOAT NULL , quantity FLOAT NULL ,
unit_concept_id INTEGER NULL , unit_concept_id INTEGER NULL ,
anatomic_site_concept_id INTEGER NULL , anatomic_site_concept_id INTEGER NULL ,
disease_status_concept_id INTEGER NULL , disease_status_concept_id INTEGER NULL ,
specimen_source_id VARCHAR(50) NULL , specimen_source_id VARCHAR(50) NULL ,
specimen_source_value VARCHAR(50) NULL , specimen_source_value VARCHAR(50) NULL ,
unit_source_value VARCHAR(50) NULL , unit_source_value VARCHAR(50) NULL ,
anatomic_site_source_value VARCHAR(50) NULL , anatomic_site_source_value VARCHAR(50) NULL ,
disease_status_source_value VARCHAR(50) NULL disease_status_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE death CREATE TABLE death
( (
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
death_date DATE NOT NULL , death_date DATE NOT NULL ,
death_type_concept_id INTEGER NOT NULL , death_datetime DATETIME2 NULL ,
cause_concept_id INTEGER NULL , death_type_concept_id INTEGER NOT NULL ,
cause_source_value VARCHAR(50) NULL, cause_concept_id INTEGER NULL ,
cause_source_concept_id INTEGER NULL cause_source_value VARCHAR(50) NULL,
) cause_source_concept_id INTEGER NULL
)
; ;
CREATE TABLE visit_occurrence CREATE TABLE visit_occurrence
( (
visit_occurrence_id INTEGER NOT NULL , visit_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
visit_concept_id INTEGER NOT NULL , visit_concept_id INTEGER NOT NULL ,
visit_start_date DATE NOT NULL , visit_start_date DATE NOT NULL ,
visit_start_time VARCHAR(10) NULL , visit_start_datetime DATETIME2 NULL ,
visit_end_date DATE NOT NULL , visit_end_date DATE NOT NULL ,
visit_end_time VARCHAR(10) NULL , visit_end_datetime DATETIME2 NULL ,
visit_type_concept_id INTEGER NOT NULL , visit_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL, provider_id INTEGER NULL,
care_site_id INTEGER NULL, care_site_id INTEGER NULL,
visit_source_value VARCHAR(50) NULL, visit_source_value VARCHAR(50) NULL,
visit_source_concept_id INTEGER NULL visit_source_concept_id INTEGER NULL
) )
; ;
CREATE TABLE procedure_occurrence CREATE TABLE procedure_occurrence
( (
procedure_occurrence_id INTEGER NOT NULL , procedure_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
procedure_concept_id INTEGER NOT NULL , procedure_concept_id INTEGER NOT NULL ,
procedure_date DATE NOT NULL , procedure_date DATE NOT NULL ,
procedure_type_concept_id INTEGER NOT NULL , procedure_datetime DATETIME2 NOT NULL ,
modifier_concept_id INTEGER NULL , procedure_type_concept_id INTEGER NOT NULL ,
quantity INTEGER NULL , modifier_concept_id INTEGER NULL ,
provider_id INTEGER NULL , quantity INTEGER NULL ,
visit_occurrence_id INTEGER NULL , provider_id INTEGER NULL ,
procedure_source_value VARCHAR(50) NULL , visit_occurrence_id INTEGER NULL ,
procedure_source_concept_id INTEGER NULL , procedure_source_value VARCHAR(50) NULL ,
qualifier_source_value VARCHAR(50) NULL procedure_source_concept_id INTEGER NULL ,
) qualifier_source_value VARCHAR(50) NULL
)
; ;
CREATE TABLE drug_exposure CREATE TABLE drug_exposure
( (
drug_exposure_id INTEGER NOT NULL , drug_exposure_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL , drug_concept_id INTEGER NOT NULL ,
drug_exposure_start_date DATE NOT NULL , drug_exposure_start_date DATE NOT NULL ,
drug_exposure_end_date DATE NULL , drug_exposure_start_datetime DATETIME2 NOT NULL ,
drug_type_concept_id INTEGER NOT NULL , drug_exposure_end_date DATE NULL ,
stop_reason VARCHAR(20) NULL , drug_exposure_end_datetime DATETIME2 NULL ,
refills INTEGER NULL , drug_type_concept_id INTEGER NOT NULL ,
quantity FLOAT NULL , stop_reason VARCHAR(20) NULL ,
days_supply INTEGER NULL , refills INTEGER NULL ,
sig VARCHAR(MAX) NULL , quantity FLOAT NULL ,
route_concept_id INTEGER NULL , days_supply INTEGER NULL ,
effective_drug_dose FLOAT NULL , sig VARCHAR(MAX) NULL ,
dose_unit_concept_id INTEGER NULL , route_concept_id INTEGER NULL ,
lot_number VARCHAR(50) NULL , effective_drug_dose FLOAT NULL ,
provider_id INTEGER NULL , dose_unit_concept_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL , lot_number VARCHAR(50) NULL ,
drug_source_value VARCHAR(50) NULL , provider_id INTEGER NULL ,
drug_source_concept_id INTEGER NULL , visit_occurrence_id INTEGER NULL ,
route_source_value VARCHAR(50) NULL , drug_source_value VARCHAR(50) NULL ,
dose_unit_source_value VARCHAR(50) NULL drug_source_concept_id INTEGER NULL ,
) route_source_value VARCHAR(50) NULL ,
dose_unit_source_value VARCHAR(50) NULL
)
; ;
CREATE TABLE device_exposure CREATE TABLE device_exposure
( (
device_exposure_id INTEGER NOT NULL , device_exposure_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
device_concept_id INTEGER NOT NULL , device_concept_id INTEGER NOT NULL ,
device_exposure_start_date DATE NOT NULL , device_exposure_start_date DATE NOT NULL ,
device_exposure_end_date DATE NULL , device_exposure_start_datetime DATETIME2 NOT NULL ,
device_type_concept_id INTEGER NOT NULL , device_exposure_end_date DATE NULL ,
unique_device_id VARCHAR(50) NULL , device_exposure_end_datetime DATETIME2 NULL ,
quantity INTEGER NULL , device_type_concept_id INTEGER NOT NULL ,
provider_id INTEGER NULL , unique_device_id VARCHAR(50) NULL ,
visit_occurrence_id INTEGER NULL , quantity INTEGER NULL ,
device_source_value VARCHAR(100) NULL , provider_id INTEGER NULL ,
device_source_concept_id INTEGER NULL visit_occurrence_id INTEGER NULL ,
) device_source_value VARCHAR(100) NULL ,
device_source_concept_id INTEGER NULL
)
; ;
CREATE TABLE condition_occurrence CREATE TABLE condition_occurrence
( (
condition_occurrence_id INTEGER NOT NULL , condition_occurrence_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
condition_concept_id INTEGER NOT NULL , condition_concept_id INTEGER NOT NULL ,
condition_start_date DATE NOT NULL , condition_start_date DATE NOT NULL ,
condition_end_date DATE NULL , condition_start_datetime DATETIME2 NOT NULL ,
condition_type_concept_id INTEGER NOT NULL , condition_end_date DATE NULL ,
stop_reason VARCHAR(20) NULL , condition_end_datetime DATETIME2 NULL ,
provider_id INTEGER NULL , condition_type_concept_id INTEGER NOT NULL ,
visit_occurrence_id INTEGER NULL , stop_reason VARCHAR(20) NULL ,
condition_source_value VARCHAR(50) NULL , provider_id INTEGER NULL ,
condition_source_concept_id INTEGER NULL visit_occurrence_id INTEGER NULL ,
) condition_source_value VARCHAR(50) NULL ,
condition_source_concept_id INTEGER NULL
)
; ;
CREATE TABLE measurement CREATE TABLE measurement
( (
measurement_id INTEGER NOT NULL , measurement_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
measurement_concept_id INTEGER NOT NULL , measurement_concept_id INTEGER NOT NULL ,
measurement_date DATE NOT NULL , measurement_date DATE NOT NULL ,
measurement_time VARCHAR(10) NULL , measurement_datetime DATETIME2 NULL ,
measurement_type_concept_id INTEGER NOT NULL , measurement_type_concept_id INTEGER NOT NULL ,
operator_concept_id INTEGER NULL , operator_concept_id INTEGER NULL ,
value_as_number FLOAT NULL , value_as_number FLOAT NULL ,
value_as_concept_id INTEGER NULL , value_as_concept_id INTEGER NULL ,
unit_concept_id INTEGER NULL , unit_concept_id INTEGER NULL ,
range_low FLOAT NULL , range_low FLOAT NULL ,
range_high FLOAT NULL , range_high FLOAT NULL ,
provider_id INTEGER NULL , provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id INTEGER NULL ,
measurement_source_value VARCHAR(50) NULL , measurement_source_value VARCHAR(50) NULL ,
measurement_source_concept_id INTEGER NULL , measurement_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL , unit_source_value VARCHAR(50) NULL ,
value_source_value VARCHAR(50) NULL value_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE note CREATE TABLE note
( (
note_id INTEGER NOT NULL , note_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
note_date DATE NOT NULL , note_date DATE NOT NULL ,
note_time VARCHAR(10) NULL , note_datetime DATETIME2 NULL ,
note_type_concept_id INTEGER NOT NULL , note_type_concept_id INTEGER NOT NULL ,
note_text VARCHAR(MAX) NOT NULL , note_text VARCHAR(MAX) NOT NULL ,
provider_id INTEGER NULL , provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id INTEGER NULL ,
note_source_value VARCHAR(50) NULL note_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE observation CREATE TABLE observation
( (
observation_id INTEGER NOT NULL , observation_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
observation_concept_id INTEGER NOT NULL , observation_concept_id INTEGER NOT NULL ,
observation_date DATE NOT NULL , observation_date DATE NOT NULL ,
observation_time VARCHAR(10) NULL , observation_datetime DATETIME2 NULL ,
observation_type_concept_id INTEGER NOT NULL , observation_type_concept_id INTEGER NOT NULL ,
value_as_number FLOAT NULL , value_as_number FLOAT NULL ,
value_as_string VARCHAR(60) NULL , value_as_string VARCHAR(60) NULL ,
value_as_concept_id INTEGER NULL , value_as_concept_id INTEGER NULL ,
qualifier_concept_id INTEGER NULL , qualifier_concept_id INTEGER NULL ,
unit_concept_id INTEGER NULL , unit_concept_id INTEGER NULL ,
provider_id INTEGER NULL , provider_id INTEGER NULL ,
visit_occurrence_id INTEGER NULL , visit_occurrence_id INTEGER NULL ,
observation_source_value VARCHAR(50) NULL , observation_source_value VARCHAR(50) NULL ,
observation_source_concept_id INTEGER NULL , observation_source_concept_id INTEGER NULL ,
unit_source_value VARCHAR(50) NULL , unit_source_value VARCHAR(50) NULL ,
qualifier_source_value VARCHAR(50) NULL qualifier_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE fact_relationship CREATE TABLE fact_relationship
( (
domain_concept_id_1 INTEGER NOT NULL , domain_concept_id_1 INTEGER NOT NULL ,
fact_id_1 INTEGER NOT NULL , fact_id_1 INTEGER NOT NULL ,
domain_concept_id_2 INTEGER NOT NULL , domain_concept_id_2 INTEGER NOT NULL ,
fact_id_2 INTEGER NOT NULL , fact_id_2 INTEGER NOT NULL ,
relationship_concept_id INTEGER NOT NULL relationship_concept_id INTEGER NOT NULL
) )
; ;
@ -483,50 +493,50 @@ Standardized health system data
CREATE TABLE location CREATE TABLE location
( (
location_id INTEGER NOT NULL , location_id INTEGER NOT NULL ,
address_1 VARCHAR(50) NULL , address_1 VARCHAR(50) NULL ,
address_2 VARCHAR(50) NULL , address_2 VARCHAR(50) NULL ,
city VARCHAR(50) NULL , city VARCHAR(50) NULL ,
state VARCHAR(2) NULL , state VARCHAR(2) NULL ,
zip VARCHAR(9) NULL , zip VARCHAR(9) NULL ,
county VARCHAR(20) NULL , county VARCHAR(20) NULL ,
location_source_value VARCHAR(50) NULL location_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE care_site CREATE TABLE care_site
( (
care_site_id INTEGER NOT NULL , care_site_id INTEGER NOT NULL ,
care_site_name VARCHAR(255) NULL , care_site_name VARCHAR(255) NULL ,
place_of_service_concept_id INTEGER NULL , place_of_service_concept_id INTEGER NULL ,
location_id INTEGER NULL , location_id INTEGER NULL ,
care_site_source_value VARCHAR(50) NULL , care_site_source_value VARCHAR(50) NULL ,
place_of_service_source_value VARCHAR(50) NULL place_of_service_source_value VARCHAR(50) NULL
) )
; ;
CREATE TABLE provider CREATE TABLE provider
( (
provider_id INTEGER NOT NULL , provider_id INTEGER NOT NULL ,
provider_name VARCHAR(255) NULL , provider_name VARCHAR(255) NULL ,
NPI VARCHAR(20) NULL , NPI VARCHAR(20) NULL ,
DEA VARCHAR(20) NULL , DEA VARCHAR(20) NULL ,
specialty_concept_id INTEGER NULL , specialty_concept_id INTEGER NULL ,
care_site_id INTEGER NULL , care_site_id INTEGER NULL ,
year_of_birth INTEGER NULL , year_of_birth INTEGER NULL ,
gender_concept_id INTEGER NULL , gender_concept_id INTEGER NULL ,
provider_source_value VARCHAR(50) NULL , provider_source_value VARCHAR(50) NULL ,
specialty_source_value VARCHAR(50) NULL , specialty_source_value VARCHAR(50) NULL ,
specialty_source_concept_id INTEGER NULL , specialty_source_concept_id INTEGER NULL ,
gender_source_value VARCHAR(50) NULL , gender_source_value VARCHAR(50) NULL ,
gender_source_concept_id INTEGER NULL gender_source_concept_id INTEGER NULL
) )
; ;
@ -539,16 +549,16 @@ Standardized health economics
************************/ ************************/
CREATE TABLE payer_plan_period CREATE TABLE payer_plan_period
( (
payer_plan_period_id INTEGER NOT NULL , payer_plan_period_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
payer_plan_period_start_date DATE NOT NULL , payer_plan_period_start_date DATE NOT NULL ,
payer_plan_period_end_date DATE NOT NULL , payer_plan_period_end_date DATE NOT NULL ,
payer_source_value VARCHAR (50) NULL , payer_source_value VARCHAR (50) NULL ,
plan_source_value VARCHAR (50) NULL , plan_source_value VARCHAR (50) NULL ,
family_source_value VARCHAR (50) NULL family_source_value VARCHAR (50) NULL
) )
; ;
@ -631,29 +641,29 @@ CREATE TABLE device_cost
*/ */
CREATE TABLE cost CREATE TABLE cost
( (
cost_id INTEGER NOT NULL , cost_id INTEGER NOT NULL ,
cost_event_id INTEGER NOT NULL , cost_event_id INTEGER NOT NULL ,
cost_domain_id VARCHAR(20) NOT NULL , cost_domain_id VARCHAR(20) NOT NULL ,
cost_type_concept_id INTEGER NOT NULL , cost_type_concept_id INTEGER NOT NULL ,
currency_concept_id INTEGER NULL , currency_concept_id INTEGER NULL ,
total_charge FLOAT NULL , total_charge FLOAT NULL ,
total_cost FLOAT NULL , total_cost FLOAT NULL ,
total_paid FLOAT NULL , total_paid FLOAT NULL ,
paid_by_payer FLOAT NULL , paid_by_payer FLOAT NULL ,
paid_by_patient FLOAT NULL , paid_by_patient FLOAT NULL ,
paid_patient_copay FLOAT NULL , paid_patient_copay FLOAT NULL ,
paid_patient_coinsurance FLOAT NULL , paid_patient_coinsurance FLOAT NULL ,
paid_patient_deductible FLOAT NULL , paid_patient_deductible FLOAT NULL ,
paid_by_primary FLOAT NULL , paid_by_primary FLOAT NULL ,
paid_ingredient_cost FLOAT NULL , paid_ingredient_cost FLOAT NULL ,
paid_dispensing_fee FLOAT NULL , paid_dispensing_fee FLOAT NULL ,
payer_plan_period_id INTEGER NULL , payer_plan_period_id INTEGER NULL ,
amount_allowed FLOAT NULL , amount_allowed FLOAT NULL ,
revenue_code_concept_id INTEGER NULL , revenue_code_concept_id INTEGER NULL ,
reveue_code_source_value VARCHAR(50) NULL reveue_code_source_value VARCHAR(50) NULL
) )
; ;
@ -666,68 +676,68 @@ Standardized derived elements
************************/ ************************/
CREATE TABLE cohort CREATE TABLE cohort
( (
cohort_definition_id INTEGER NOT NULL , cohort_definition_id INTEGER NOT NULL ,
subject_id INTEGER NOT NULL , subject_id INTEGER NOT NULL ,
cohort_start_date DATE NOT NULL , cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL cohort_end_date DATE NOT NULL
) )
; ;
CREATE TABLE cohort_attribute CREATE TABLE cohort_attribute
( (
cohort_definition_id INTEGER NOT NULL , cohort_definition_id INTEGER NOT NULL ,
cohort_start_date DATE NOT NULL , cohort_start_date DATE NOT NULL ,
cohort_end_date DATE NOT NULL , cohort_end_date DATE NOT NULL ,
subject_id INTEGER NOT NULL , subject_id INTEGER NOT NULL ,
attribute_definition_id INTEGER NOT NULL , attribute_definition_id INTEGER NOT NULL ,
value_as_number FLOAT NULL , value_as_number FLOAT NULL ,
value_as_concept_id INTEGER NULL value_as_concept_id INTEGER NULL
) )
; ;
CREATE TABLE drug_era CREATE TABLE drug_era
( (
drug_era_id INTEGER NOT NULL , drug_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL , drug_concept_id INTEGER NOT NULL ,
drug_era_start_date DATE NOT NULL , drug_era_start_date DATE NOT NULL ,
drug_era_end_date DATE NOT NULL , drug_era_end_date DATE NOT NULL ,
drug_exposure_count INTEGER NULL , drug_exposure_count INTEGER NULL ,
gap_days INTEGER NULL gap_days INTEGER NULL
) )
; ;
CREATE TABLE dose_era CREATE TABLE dose_era
( (
dose_era_id INTEGER NOT NULL , dose_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
drug_concept_id INTEGER NOT NULL , drug_concept_id INTEGER NOT NULL ,
unit_concept_id INTEGER NOT NULL , unit_concept_id INTEGER NOT NULL ,
dose_value FLOAT NOT NULL , dose_value FLOAT NOT NULL ,
dose_era_start_date DATE NOT NULL , dose_era_start_date DATE NOT NULL ,
dose_era_end_date DATE NOT NULL dose_era_end_date DATE NOT NULL
) )
; ;
CREATE TABLE condition_era CREATE TABLE condition_era
( (
condition_era_id INTEGER NOT NULL , condition_era_id INTEGER NOT NULL ,
person_id INTEGER NOT NULL , person_id INTEGER NOT NULL ,
condition_concept_id INTEGER NOT NULL , condition_concept_id INTEGER NOT NULL ,
condition_era_start_date DATE NOT NULL , condition_era_start_date DATE NOT NULL ,
condition_era_end_date DATE NOT NULL , condition_era_end_date DATE NOT NULL ,
condition_occurrence_count INTEGER NULL condition_occurrence_count INTEGER NULL
) )
; ;